Biologists who study the relationships between animal groups are known as taxonomists, and they have a wide array of tools at their disposal for determining the exact phylogeny of organisms. Among these are gross anatomy, protein similarity and direct gene sequencing, as related by Rediscovering Biology.
One method of classifying organisms dates to the dawn of classical taxonomy and involves a gross anatomical comparison between the physical traits of living things. The similarities between them can thus be plotted into a rough tree of likely kinship between species. According to Rediscovering Biology, this method works well with the classical system that was first developed by Charles Linn in the 18th century.
A more modern method, and one that takes into account the true evolutionary relationships between living things, is known as cladism. This method aims at developing a true tree of life that can be useful for identifying the history and relationships of organisms. This system often relies on direct analysis of gross anatomy, as with classical taxonomy, as well as examination of the organism on a molecular level to compare proteins. According to Rediscovering Biology, cladists sometimes resort to a direct, point-by-point comparison of organisms' nucleotide sequences for clues to their true heritage.